In our 1 M GWAS, 4 of the 10 SNPs most significantly associated with body mass index (BMI) mapped near or within the MAP2K3 gene. Fine mapping of this region revealed that specific regions of this locus were duplicated, and a large number of the database SNPs from this region were false SNPs. Validated SNPs that mapped uniquely to the MAP2K3 locus were genotyped in 3500 full-heritage Pima Indians and replication was assessed in a second sample of 3800 American Indians. Two tag SNPs were associated with BMI in the full-heritage Pima sample and the associations replicated in the second sample. The effect of specific variants on BMI in Caucasians was evaluated using genotypic data from the GIANT consortium. One of the tag SNPs was additionally associated with BMI among 123,800 Caucasians, suggesting that variation in MAP2K3 affects BMI in multiple ethnic groups. Also among the top GWAS signals for BMI were 3 variants that mapped within the lysophosphatidylglycerol acyltransferase 1 (LPGAT1) gene. LPGAT1 belongs to a large family of acyltransferases which are involved in a variety of biological processes including pathways that regulate energy homeostasis and body weight. Therefore LPGAT1 was analyzed as a candidate gene for obesity in Pima Indians. Variants (n = 26) located within and adjacent to LPGAT1 including a novel 27 bp deletion identified by sequencing were genotyped in a population-based sample of 3391 full-heritage Pima Indians living in the Gila River Indian Community. Replication of selected variants was assessed in a second sample of 3327 mixed-heritage Native Americans from the same community. Variants with nominal associations with body mass index (BMI) in each of the two independent samples (tagged by rs112662024 and rs12058008) had associations of P = 1-4 x 10-5 in the combined sample (n = 6718). A haplotype that included a novel 27 bp deletion, which does not occur in Caucasians, showed the strongest association with BMI in full heritage Pima Indians. In vitro functional analysis provided suggestive evidence that this 27 bp deletion in the 5-UTR may affect transcriptional or post-transcriptional regulation. Analysis of LPGAT1 cDNA from human preadipocytes identified an additional exon whose sequence could potentially serve as a mitochondrial targeting peptide.